cboettig
commented
9 years ago Looks like your testing system doesn't have the Suggested dependencies for RNeXML installed -- java libraries in this case. I've only recently fixed a bug wrt pre-installing these java libraries on the docker images
On Tue, Dec 9, 2014, 7:59 AM Scott Chamberlain notifications@github.com wrote:
I just checked devtools::revdep_check(), and I get for RNeXML (this doesn't seem like a problem with taxize, but i wasn't sure):
- using log directory ‘/private/var/folders/gs/4khph0xs0436gmd2gdnwsg080000gn/T/RtmpMsC2do/check_cran52d34045f85/RNeXML.Rcheck’
- using R version 3.1.2 (2014-10-31)
- using platform: x86_64-apple-darwin13.4.0 (64-bit)
- using session charset: UTF-8
- using option ‘--no-codoc’
- checking for file ‘RNeXML/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘RNeXML’ version ‘2.0.0’
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘RNeXML’ can be installed ... [10s/10s] OK
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... WARNING ---- unloading Error in .mergeMethodsTable(generic, mtable, get(tname, envir = env), : trying to get slot "defined" from an object of a basic class ("environment") with no slots Calls: unloadNamespace ...
-> .updateMethodsInTable -> .mergeMethodsTable Execution halted - checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... SKIPPED
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [16s/16s] OK
- checking for unstated dependencies in tests ... OK
checking tests ... ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: 0 taxonomic units Taxa: ...
NeXML generated by RNeXML using schema version: 0.9 size: 21.7 Kb
parsing : ... publish : Authentication successful 5 rdf : Loading required package: Sxslt .Loading required package: rrdf Loading required package: rJava No Java runtime present, requesting install.
— Reply to this email directly or view it on GitHub https://github.com/ropensci/RNeXML/issues/105.
sckott
I just checked
devtools::revdep_check(), and I get forRNeXML(this doesn't seem like a problem with taxize, but i wasn't sure):